Lysine-Isoleucine-Arginine-Alanine wrote:What is the longest English word you can spell using the one letter abbreviations of the 20 genetic amino acids? What about the three letter abbreviations? What would the resultant peptides look like?

There may not be a lot of real English words to be made from those TLAs (Randall did miss hisser), but I see a rich vein of second-order sniglets. ("Words that should be in the list of sniglets, but aren't.") E.g., phegly, promet, proalacys, thrasp, argile, leuser, gluser.

With rare but extant Selenocysteine (O) and Pyrrolysine (U) and without the colonial spelling, "Deinsitutionalisation" is a perfectly cromulant peptide chain... Or is that a Pyrrolysine-Valene-Glutamic Acid-Arginine-Isoleucine-Asparagine-Threonine-Glutamic Acid-Arginine-Leucine-Glutamic Acid-Cysteine-Threonine-Selenoceistine-Alanine-Leucine-Isoleucine-Serine-Alanine-Threonine-Isoleucine-Pyrrolysine-Aspargine?

Did Randall purposefully interpret "what about the three-letter abbreviations" as "the three-letter sequences" rather than "the letters used in the three-letter abbreviations"?He did interpret "using the one-letter abbreviations" as "any multiplicity of the set of letters that occur in the abbreviations" rather than "pick letters from the list" or "make words with exactly all the aminoacids occuring once".

In any case you can't spell Flumble, so I'll have to develop a virus which encodes for tRNA variations that accept new aminoacids and which hacks into the genome to produce a FLUMBLE sequence after every stop codon. Including the codon(s) in the virus of course.

HES wrote:If there are only 20 genetic amino acids, and they have distinct one-letter abbreviations, why bother having three-letter abbreviations?

The three-letter ones use letters that correspond to the name of the amino acid. Now one could say that's not terribly helpful because the names of the amino acids are also made-up nonsense (unless you know the etymology), but it seems like people in the field like to remember names rather than single letters.

Or maybe the three-letter abbreviations are designed for forward compatibility. Researchers are incorporating other amino acids in synthetic biology, so maybe we'll see aditions to the proteinogenic list in the future.

In 1995, researchers isolated several proteins produced during these infections, looking for possible targets for antibodies. One of the proteins they found was WYSLNGKIRAVDVPK, or GKIRAV for short.

...The bad news is that the researchers filed a patent which includes this sequence. The patent, published in 1999, gives the researchers exclusive control over this protein. If Kira wants to mess around with the protein, she could—in theory—be sued.

The good news is that in 2013, the Supreme Court struck down this type of gene patent. The case, Association for Molecular Pathology v. Myriad Genetics, Inc., involved the patents protecting tests for genetic cancer risk. That means Kira is totally free to produce as much WYSLNGKIRAVDVPK as she wants.

Wrong on so many levels.

Firstly, the patent was filed, based on a PCT filed in the UK, in many other countries than the US, with the first document in the patent family being published in 1995. We aren't told where Kira comes from so it isn't clear that the US patent would be the one relevant to her research, or even that she comes from a place in which a patent has been granted.

Secondly, the US, like many other jurisdictions, has a research exemption that allows research to be carried out on the patented subject matter for certain purposes. This exception is narrow in the US (my understanding is it only covers research for the purpose of getting approvals) but in other countries it is broader.

Thirdly, whilst some of the independent claims are directed to a purified bacterial protein expressed during infection due to streptococci, and this at least appears to be a compound found in nature of the type found unelligible in Myriad, it is not entirely clear that all of the claims (particularly claim 10) are of this nature. Not being a biologist it is hard for me to say, but a claim to recombinant DNA (which I understand is made in the lab) would seem not to fall within this exception unless that DNA is already found in nature.

Fourthly, any and all of the above is moot because the patent should have already expired.

Durandal_1707 wrote:Hey, I caught a typo! "Deinstitutionalization," not "deinsitutionalization." As written, it would only have been 21 letters, not 22.

Ahhh.. I saw that it wasn't based upon "institute", but: a) didn't count the letters, and b) didn't for one moment think that making it "...institut.." rather than "...insitut.." (the latter something I'd considered rooted upon the same root as "situational") would have made it one better... Fail on my part.

But does this open up even longer words*? I don't know. Maybe you'd have to ask a counterantidisensituationalisationistish person for their point of view..?

* Using UK spelling, and allowing the 21st/22nd O and U peptides, as noted, of course.

WhoopsThis article is still in progress. An early draft was unintentionally posted here thanks to Randall's troubled approach to git, and it took a little bit to get everything sorted out and rolled back. Sorry for the mixup!

WhoopsThis article is still in progress. An early draft was unintentionally posted here thanks to Randall's troubled approach to git, and it took a little bit to get everything sorted out and rolled back. Sorry for the mixup!

Soupspoon wrote:With rare but extant Selenocysteine (O) and Pyrrolysine (U) and without the colonial spelling, "Deinsitutionalisation" is a perfectly cromulant peptide chain...

Well, geez, if you're going to do that then you can do "pneumonoultramicroscopicsilicovolcanoconiosis" (45 letters) Or if you want a word that wasn't originally coined to be a long word, "dichlorodiphenyltrichloroethane" (31 letters). Or if you want ones that aren't chemicals, "electroencephalographically" and "microspectrophotometrically" (27 letters)

If we apply that to the other challenge (adding in SEC and UAG).... hmm, it actually doesn't add anything longer to the list, or even a new six-letter word. We could get up to nine letters if someone would invent amino acids with the following TLAs:

WhoopsThis article is still in progress. An early draft was unintentionally posted here thanks to Randall's troubled approach to git, and it took a little bit to get everything sorted out and rolled back. Sorry for the mixup!